Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

Dolores Rita Agius, Aliki Kapazoglou, Evangelia Avramidou, Miroslav Baranek, Elena Carneros, Elena Caro, Stefano Castiglione, Angela Cicatelli, Aleksandra Radanovic, Jean Paul Ebejer, Daniel Gackowski, Francesco Guarino, Andrea Gulyás, Norbert Hidvégi, Hans Hoenicka, Vera Inácio, Frank Johannes, Erna Karalija, Michal Lieberman-Lazarovich, Federico MartinelliStéphane Maury, Velimir Mladenov, Leonor Morais-Cecílio, Ales Pecinka, Eleni Tani, Pilar S. Testillano, Dimitar Todorov, Luis Valledor, Valya Vassileva

Research output: Contribution to journalReview articlepeer-review

10 Scopus citations

Abstract

Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.

Original languageEnglish
Article number1181039
JournalFrontiers in Plant Science
Volume14
DOIs
StatePublished - 2023

Keywords

  • DNA methylation modulation
  • DNA methylation profiling
  • bisulfite sequencing
  • crop epigenome
  • immunological techniques
  • mass spectrometry
  • next-generation sequencing

Fingerprint

Dive into the research topics of 'Exploring the crop epigenome: a comparison of DNA methylation profiling techniques'. Together they form a unique fingerprint.

Cite this